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Complete plasmid sequences for all B. thuringiensis strains were extracted from RefSeq plasmid and were converted into blast database.
Contig sequences were then searched against the custome DB using BLAST+ (blastn). Contigs with query coverages >= 95% were chosen for putative plasmidic sequences.
Commands for blast search
blastn -query BP865_KRIBB.fna -db Bt_plasmid.fna -outfmt "6 std qcovs" -num_threads 30 -out out_BP865 blastn -query BTaizawai_KRIBB.fna -db Bt_plasmid.fna -outfmt "6 std qcovs" -num_threads 30 -out out_BTaizawai
Using different cutoff values
Putative plasmid sequences